The Nobel committee called the pair "representatives of all journalists who stand up for this ideal".
The winners of the prestigious prize, worth 10m Swedish krona (£836,000; $1.1m), were announced at the Norwegian Nobel Institute in Oslo.
They were chosen out of 329 candidates.
Ms Ressa, who co-founded the news site Rappler, was commended for using freedom of expression to "expose abuse of power, use of violence and growing authoritarianism in her native country, the Philippines".
In a live broadcast by Rappler, Ms Ressa said she was "in shock".
The Nobel committee said Mr Muratov, the co-founder and editor of independent newspaper Novaya Gazeta, had for decades defended freedom of speech in Russia under increasingly challenging conditions.